check --repair: re-read only the packs the repair wrote, refs #8466

[mr-raj12]

Description

Refs #8466, item 2 of #10318. Based on #10368, only the last commit is new.

With #10368, the checker and the repository share one chunk index, and put() / delete() update it for every pack they write. So ArchiveChecker.finish() no longer rebuilds the index from all packs after a repair that changed packs. It re-reads only the packs the repair wrote.

• ArchiveChecker records the packs repair writes in written_packs: from the put() and flush() results, and from delete(), which now returns compact_pack()'s (new_pack_id, dropped_bytes). A pack rewritten again is replaced by its new pack.
• create_archive_entry() flushes before Archives.create(), which flushes and discards the results.
• verify_written_packs() walks each written pack with a validator and compares it with the index:
  • an index entry the pack does not hold: removed from the index
  • an object whose chunk id is not indexed: added to the index
  • a written pack that is missing: its index entries are removed
  • each of these is a finding
  • an object whose chunk id is already indexed (a superseded duplicate) is not a finding
• If check() built the index without a validator (the key could not be read), finish() still rebuilds the index from all packs with a validator.
• finish() drops the index in one place for both paths (invalidate_chunk_index() and self.chunks = None), before the full rebuild.
• Repository.flush() returns the pack writer's flush results.

Tests (check_cmd_test.py):

• finish() reads only the rewritten pack, the packs put() wrote, and the pack its own flush() stores.
• Without the key, finish() rebuilds from all packs.
• A defect chunk alone in its pack: delete() drops the pack and finish() re-reads no pack.
• A rewritten pack holding an object no index entry names, a superseded duplicate, a wrong index entry, and a missing written pack.
• test_check_holds_a_single_chunk_index: a case for the full rebuild in finish(), asserting the checker's index is freed first.

Tests (repository_test.py): flush() returns the stored objects, or None with nothing buffered or no pack writer.

Full test suite: 3093 passed, 1142 skipped.

Checklist

• PR is against master (or maintenance branch if only applicable there)
• New code has tests and docs where appropriate
• Tests pass (run tox or the relevant test subset)
• Commit messages are clean and reference related issues

[codecov]

Codecov Report

❌ Patch coverage is 98.94737% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 88.14%. Comparing base (3b905e0) to head (74fcb2b).
⚠️ Report is 35 commits behind head on master.
✅ All tests successful. No failed tests found.

Files with missing lines	Patch %	Lines
src/borg/archive.py	98.90%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master   #10379      +/-   ##
==========================================
+ Coverage   88.12%   88.14%   +0.02%     
==========================================
  Files         103      103              
  Lines       18928    18910      -18     
  Branches     2923     2928       +5     
==========================================
- Hits        16681    16669      -12     
- Misses       1556     1557       +1     
+ Partials      691      684       -7     

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